Mercurial > repos > devteam > ncbi_blast_plus
changeset 33:d999e774072a draft
Fix for get_species_taxids
| author | peterjc |
|---|---|
| date | Sun, 19 Nov 2023 22:57:39 +0000 |
| parents | a52d2d93e595 |
| children | b6893f57f8d8 |
| files | tools/ncbi_blast_plus/get_species_taxids.xml tools/ncbi_blast_plus/ncbi_macros.xml |
| diffstat | 2 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/tools/ncbi_blast_plus/get_species_taxids.xml Thu Oct 26 12:25:07 2023 +0000 +++ b/tools/ncbi_blast_plus/get_species_taxids.xml Sun Nov 19 22:57:39 2023 +0000 @@ -7,17 +7,17 @@ <command detect_errors="aggressive"><![CDATA[ #if $type_cond.type_sel == 'names' #for name in $type_cond.names.split(',') - taxid=\$(get_species_taxids.sh -n '$name' | grep Taxid | sed 's/Taxid://') && - if [ -z \$taxid ]; then + taxid=\$(get_species_taxids.sh -n '$name' | grep Taxid | sed 's/Taxid\s*:\s*//') && + if [ -z "\$taxid" ]; then >&2 echo "could not find taxid for $name" && exit 1; else echo " $name -> \$taxid"; fi && - get_species_taxids.sh -t \$taxid >> species_ids.txt && + get_species_taxids.sh -t "\$taxid" >> species_ids.txt && #end for #else #for taxid in $type_cond.ids.split(',') - get_species_taxids.sh -t $taxid >> species_ids.txt && + get_species_taxids.sh -t "$taxid" >> species_ids.txt && #end for #end if sort -n -u species_ids.txt > '$output'
--- a/tools/ncbi_blast_plus/ncbi_macros.xml Thu Oct 26 12:25:07 2023 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Sun Nov 19 22:57:39 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.14.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">16.10</token> <xml name="parallelism"> <!-- If job splitting is enabled, break up the query file into parts -->